Molecular Epidemiology and Virus Genomics

Genomic data analysis

We analyze genetic and genomic data to understand the transmission and evolution of viruses with a focus on HIV. With a broad comparative analysis we demonstrated that guanine-adenine bias is a general property of the codon usage of retroid viruses, unrelated to host-induced hypermutation. Analyzing a large European dataset we showed that superinfection with drug-resistant HIV-1 strains does not significantly contribute to the spread of drug resistance. We also investigated the prevalence of transmitted drug resistance and transmission dynamics in newly diagnosed, treatment-naïve HIV-positive patients in Hungary. Following up on such studies, in 2025 we performed the most comprehensive molecular epidemiological characterization of the Hungarian HIV-1 epidemic, where we characterized the domestic and international spread of viral lineages.

In recent years, we also contributed to the molecular epidemiology of other viruses in Hungary, including Hepatitis E and Hantaviruses.

Virus genomics method development

To guide the choice of bioinformatics pipelines for assembling full-length viral genomes from next-generation sequencing data, we benchmarked the most popular open-source hybrid genome assembly pipelines and published a user-friendly containerized version of the shiver pipeline.

Relevant publications

  • Müller, V.; Bonhoeffer, S. Guanine–Adenine Bias: A General Property of Retroid Viruses That Is Unrelated to Host-Induced Hypermutation. Trends in Genetics 2005, 21, 264–268, doi:10.1016/j.tig.2005.03.004.
  • Bartha, I.; Assel, M.; Sloot, P.M.; Zazzi, M.; Torti, C.; Schülter, E.; Luca, A.D.; Sönnerborg, A.; Abecasis, A.B.; Van Laethem, K.; et al. Superinfection with Drug-Resistant HIV Is Rare and Does Not Contribute Substantially to Therapy Failure in a Large European Cohort. BMC Infect Dis 2013, 13, 537, doi:10.1186/1471-2334-13-537.
  • Áy, É.; Müller, V.; Mezei, M.; Pocskay, Á.; Koroknai, A.; Müller, D.; Győri, Z.; Marschalkó, M.; Tóth, B.; Kárpáti, S.; et al. Transmitted Drug Resistance in Newly Diagnosed and Treatment-Naïve HIV Type 1-Infected Patients in Hungary. Journal of Global Antimicrobial Resistance 2020, 20, 124–130, doi:10.1016/j.jgar.2019.07.014.
  • Zsichla, L.; Zeeb, M.; Fazekas, D.; Áy, É.; Müller, D.; Metzner, K.J.; Kouyos, R.D.; Müller, V. Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly. Viruses 2024, 16, 1824, doi:10.3390/v16121824.
  • Zsichla, L.; Adravecz, L.; Müller, D.; Lemey, P.; Lakatos, Á.; Ari, E.; Kusejko, K.; Kouyos, R.; Szlávik, J.; Lakatos, B.; et al. Molecular Epidemiology of HIV-1 in Hungary: An Evolving Contact Zone of Colliding Virus Subtypes. Front. Microbiol. 2025, 16, doi:10.3389/fmicb.2025.1732254.
  • Dencs, Á.; Hettmann, A.; Zsichla, L.; Müller, V.; Dömötör, A.; Barna-Lázár, Á.; Barcsay, E.; Takács, M. Molecular Epidemiology of Hepatitis E Virus in Hungary (2018–2025): Emergence of Rare Subtypes and First Detection of HEV-4 in Central Europe. Viruses 2025, 17, 1389, doi:10.3390/v17101389.
  • Koroknai, A.; Nagy, A.; Nagy, O.; Csonka, N.; Zsichla, L.; Szomor, K.; Takács, M. Human Hantavirus Infections in Hungary (2018–2025): Epidemiology, Molecular Detection Across Clinical Sample Types, and Phylogenetic Analysis. Viruses 2026, 18, doi:10.3390/v18030366.

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